forked from D-Net/dnet-hadoop
added step for observatory db
This commit is contained in:
parent
25d0512fbd
commit
625d993cd9
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export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
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export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
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if ! [ -L $link_folder ]
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then
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rm -Rf "$link_folder"
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ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
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fi
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export SOURCE=$1
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export TARGET=$2
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export SHADOW=$3
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export SCRIPT_PATH=$4
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echo "Getting file from " $4
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hdfs dfs -copyToLocal $4
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echo "Creating observatory database"
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impala-shell -q "drop database if exists ${TARGET} cascade"
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impala-shell -q "create database if not exists ${TARGET}"
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impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${TARGET}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -f -
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cat step21-createObservatoryDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f -
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echo "Impala shell finished"
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echo "Updating shadow observatory database"
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impala-shell -q "create database if not exists ${SHADOW}"
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impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f -
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impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${TARGET}.\1;/" | impala-shell -f -
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echo "Shadow db ready!"
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@ -0,0 +1,259 @@
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create table TARGET.result_affiliated_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, c.code, c.name;
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create table TARGET.result_affiliated_year stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, r.year
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, r.year;
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create table TARGET.result_affiliated_year_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, r.year, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, r.year, c.code, c.name;
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create table TARGET.result_affiliated_datasource stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, d.name as dname
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_datasources rd on rd.id=r.id
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left outer join SOURCE.datasource d on d.id=rd.datasource
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, d.name;
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create table TARGET.result_affiliated_datasource_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, d.name as dname, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_datasources rd on rd.id=r.id
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left outer join SOURCE.datasource d on d.id=rd.datasource
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, d.name, c.code, c.name;
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create table TARGET.result_affiliated_organization stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, o.name as oname
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, o.name;
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create table TARGET.result_affiliated_organization_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, o.name as oname, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, o.name, c.code, c.name;
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create table TARGET.result_affiliated_funder stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, p.funder as pfunder
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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join SOURCE.result_projects rp on rp.id=r.id
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join SOURCE.project p on p.id=rp.project
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, p.funder;
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create table TARGET.result_affiliated_funder_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, p.funder as pfunder, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_organization ro on ro.id=r.id
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join SOURCE.organization o on o.id=ro.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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join SOURCE.result_projects rp on rp.id=r.id
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join SOURCE.project p on p.id=rp.project
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, p.funder, c.code, c.name;
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create table TARGET.result_deposited_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, c.code, c.name;
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create table TARGET.result_deposited_year stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, r.year
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, r.year;
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create table TARGET.result_deposited_year_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, r.year, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, r.year, c.code, c.name;
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create table TARGET.result_deposited_datasource stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, d.name as dname
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, d.name;
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create table TARGET.result_deposited_datasource_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, d.name as dname, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, d.name, c.code, c.name;
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create table TARGET.result_deposited_organization stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa, r.peer_reviewed, r.type, o.name as oname
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, o.name;
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create table TARGET.result_deposited_organization_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, o.name as oname, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, o.name, c.code, c.name;
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create table TARGET.result_deposited_funder stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, p.funder as pfunder
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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join SOURCE.result_projects rp on rp.id=r.id
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join SOURCE.project p on p.id=rp.project
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
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group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, p.funder;
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create table TARGET.result_deposited_funder_country stored as parquet as
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select count(distinct r.id) as total, r.green, r.gold, case when rl.type is not null then true else false end as licence,
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case when pids.pid is not null then true else false end as pid, case when r.access_mode in ('Open Access', 'Open Source') then true else false end as oa,
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r.peer_reviewed, r.type, p.funder as pfunder, c.code as ccode, c.name as cname
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from SOURCE.result r
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join SOURCE.result_datasources rd on rd.id=r.id
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join SOURCE.datasource d on d.id=rd.datasource and d.type in ('Institutional Repository','Data Repository', 'Repository', 'Publication Repository')
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join SOURCE.datasource_organizations dor on dor.id=d.id
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join SOURCE.organization o on o.id=dor.organization
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join SOURCE.country c on c.code=o.country and c.continent_name='Europe'
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join SOURCE.result_projects rp on rp.id=r.id
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join SOURCE.project p on p.id=rp.project
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left outer join SOURCE.result_licenses rl on rl.id=r.id
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left outer join SOURCE.result_pids pids on pids.id=r.id
|
||||
group by r.green, r.gold, licence, pid, oa, r.peer_reviewed, r.type, p.funder, c.code, c.name;
|
||||
|
||||
compute stats TARGET.result_affiliated_country;
|
||||
compute stats TARGET.result_affiliated_year;
|
||||
compute stats TARGET.result_affiliated_year_country;
|
||||
compute stats TARGET.result_affiliated_datasource;
|
||||
compute stats TARGET.result_affiliated_datasource_country;
|
||||
compute stats TARGET.result_affiliated_organization;
|
||||
compute stats TARGET.result_affiliated_organization_country;
|
||||
compute stats TARGET.result_affiliated_funder;
|
||||
compute stats TARGET.result_affiliated_funder_country;
|
||||
compute stats TARGET.result_deposited_country;
|
||||
compute stats TARGET.result_deposited_year;
|
||||
compute stats TARGET.result_deposited_year_country;
|
||||
compute stats TARGET.result_deposited_datasource;
|
||||
compute stats TARGET.result_deposited_datasource_country;
|
||||
compute stats TARGET.result_deposited_organization;
|
||||
compute stats TARGET.result_deposited_organization_country;
|
||||
compute stats TARGET.result_deposited_funder;
|
||||
compute stats TARGET.result_deposited_funder_country;
|
||||
|
|
@ -25,6 +25,14 @@
|
|||
<name>monitor_db_shadow_name</name>
|
||||
<description>the name of the shadow monitor db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>observatory_db_name</name>
|
||||
<description>the target monitor db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>observatory_db_shadow_name</name>
|
||||
<description>the name of the shadow monitor db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>stats_tool_api_url</name>
|
||||
<description>The url of the API of the stats tool. Is used to trigger the cache update.</description>
|
||||
|
|
@ -305,11 +313,26 @@
|
|||
<argument>${wf:appPath()}/scripts/step20-createMonitorDB.sql</argument>
|
||||
<file>monitor.sh</file>
|
||||
</shell>
|
||||
<ok to="Step21"/>
|
||||
<ok to="step21-createObservatoryDB"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Step21">
|
||||
<action name="step21-createObservatoryDB">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>observatory.sh</exec>
|
||||
<argument>${stats_db_name}</argument>
|
||||
<argument>${observatory_db_name}</argument>
|
||||
<argument>${observatory_db_shadow_name}</argument>
|
||||
<argument>${wf:appPath()}/scripts/step21-createObservatoryDB.sql</argument>
|
||||
<file>observatory.sh</file>
|
||||
</shell>
|
||||
<ok to="Step22"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Step22">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
|
|
|
|||
Loading…
Reference in New Issue